![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10013 closed defect (duplicate)
Crash in Qt event loop: QPainter::begin: Paint device returned engine == 0, type: 3
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000031e4bf000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031d4bc000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031c4b9000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031b4b6000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031a4b3000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003194b0000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003184ad000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003174aa000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003164a7000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003154a4000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003144a1000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000202898600 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-10-17 18:53:28.00 -0700","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"AD706ED2-63EF-4D8C-AB5D-96886A6782A9","name":"ChimeraX"}
{
"uptime" : 930000,
"procLaunch" : "2023-10-17 14:57:32.7373 -0700",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 22018659657488,
"coalitionID" : 2241,
"osVersion" : {
"train" : "macOS 12.2.1",
"build" : "21D62",
"releaseType" : "User"
},
"captureTime" : "2023-10-17 18:51:06.6238 -0700",
"incident" : "AD706ED2-63EF-4D8C-AB5D-96886A6782A9",
"bug_type" : "309",
"pid" : 30766,
"procExitAbsTime" : 22354967163067,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"58B789E1-901A-570B-A658-90F4780909CF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C3F0725F-111E-2832-B2B0-4ABB44C5B9F5",
"wakeTime" : 28370,
"sleepWakeUUID" : "7CCEC93C-F771-4E06-A7BF-D2F1B31265CC",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4334497768\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1025b3000-1025b4000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4334497768\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1025b3000-1025b4000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":68198080,"threadState":{"flavor":"x86_THREAD_STATE","rbp":{"value":14422827625862724185},"r12":{"value":259},"rosetta":{"tmp2":{"value":140703362941192},"tmp1":{"value":140705784916244},"tmp0":{"value":18446744073709551615}},"rbx":{"value":8632501760,"symbolLocation":0,"symbol":"_main_thread"},"r8":{"value":11},"r15":{"value":22},"r10":{"value":8632501760,"symbolLocation":0,"symbol":"_main_thread"},"rdx":{"value":0},"rdi":{"value":14422827625862724185},"r9":{"value":14422827625862724185},"r13":{"value":5},"rflags":{"value":643},"rax":{"value":0},"rsp":{"value":4475646088},"r11":{"value":140703363712422,"symbolLocation":0,"symbol":"-[__NSCFArray 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"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
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"base" : 4549046272,
"size" : 8192,
"uuid" : "1eae6074-8612-3bc6-b16b-c173a995e90c",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
"name" : "_queue.cpython-39-darwin.so"
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"base" : 140703407054848,
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15278080,
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"name" : "AppKit",
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"base" : 4574330880,
"size" : 64028672,
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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}
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"sharedCache" : {
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"size" : 15218196480,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 768K 6 \nActivity Tracing 256K 1 \nCG backing stores 1536K 8 \nCG image 700K 80 \nColorSync 240K 28 \nCoreAnimation 5100K 162 \nCoreGraphics 12K 2 \nCoreUI image data 6808K 69 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.6G 741 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 616.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1544K 383 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 900K 90 \nRosetta Thread Context 900K 90 \nSTACK GUARD 36K 9 \nStack 328.7M 46 \nStack Guard 56.2M 37 \nVM_ALLOCATE 191.9M 391 \nVM_ALLOCATE (reserved) 128.1M 14 reserved VM address space (unallocated)\n__DATA 43.9M 674 \n__DATA_CONST 30.3M 344 \n__DATA_DIRTY 1641K 218 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 730.9M 155 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 790.7M 676 \n__UNICODE 588K 1 \ndyld private memory 1056K 3 \nmapped file 5.6G 1185 \nshared memory 3036K 33 \nunshared pmap 10.3M 8 \n=========== ======= ======= \nTOTAL 10.4G 5493 \nTOTAL, minus reserved VM space 9.6G 5493 \n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/lauriewang/Library/CloudStorage/GoogleDrive-
> lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/4. Substrate-engaged
> inhibitor bound ChiSec61/3. Structural
> modeling/J309_Sec61-KZR779-coot-9_conf1_real_space_refined_001.pdb"
Chain information for
J309_Sec61-KZR779-coot-9_conf1_real_space_refined_001.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> set bgColor white
> lighting soft
> style ball
Changed 4250 atom styles
> select /A:501@C30
Nothing selected
> select 1/A:501@C30
Expected an objects specifier or a keyword
> select #1/A:501@C30
Nothing selected
> color /A,B,C gray
> color /A:501@C58@O09@C57@C55@C53@C56@C54@C52@C49@C45@N13@C47@C50 blue
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:468
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:410-468
443 atoms, 450 bonds, 59 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:65
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /C
244 atoms, 251 bonds, 31 residues, 1 model selected
> select /A:6-7
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:6-43
319 atoms, 327 bonds, 38 residues, 1 model selected
> select /A:468
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:351-468
901 atoms, 919 bonds, 118 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B
480 atoms, 489 bonds, 61 residues, 1 model selected
> open "/Users/lauriewang/Library/CloudStorage/GoogleDrive-
> lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/4. Substrate-engaged
> inhibitor bound ChiSec61/3. Structural
> modeling/J309_Sec61-KZR779-coot-9_conf2_real_space_refined_001.pdb"
Chain information for
J309_Sec61-KZR779-coot-9_conf2_real_space_refined_001.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A
Alignment identifier is 1
> select #1/A:399-400 #2/A:399-400
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #1/A:346-399 #2/A:346-399
832 atoms, 856 bonds, 108 residues, 2 models selected
1 [ID: 1] region 2 chains [327-380] RMSD: 0.000
> select #1/A:432-433 #2/A:432-433
26 atoms, 24 bonds, 4 residues, 2 models selected
> select #1/A:432-457 #2/A:432-457
374 atoms, 378 bonds, 52 residues, 2 models selected
1 [ID: 1] region 2 chains [413-438] RMSD: 0.000
> select #1/A:457-458 #2/A:457-458
46 atoms, 48 bonds, 4 residues, 2 models selected
> select #1/A:457-468 #2/A:457-468
214 atoms, 218 bonds, 24 residues, 2 models selected
1 [ID: 1] region 2 chains [438-449] RMSD: 0.000
> hide #2.1 models
> show #2.1 models
> select add #2.1
214 atoms, 218 bonds, 2 pseudobonds, 24 residues, 3 models selected
> select subtract #2.1
214 atoms, 218 bonds, 24 residues, 2 models selected
> select #1/A:351-468
901 atoms, 919 bonds, 118 residues, 1 model selected
> select add #2
5151 atoms, 5262 bonds, 2 pseudobonds, 660 residues, 3 models selected
> hide #!1 models
> show #!1 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #2.1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #2
> show #!1 models
> show #1.1 models
> color /A:501@C58@O09@C57@C55@C53@C56@C54@C52@C49@C45@N13@C47@C50 blue
> select /A:501
58 atoms, 62 bonds, 1 residue, 1 model selected
> color /A:62-71 violet
> color /A:292,183,179,81,85 saddle brown
> color /A:300 orange
> color /A:127 orangered
> color /A:300,127 byhetero
> volume zone #2 nearAtoms #1/A:501 range 2 newMap true
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /A:462
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:462-467
49 atoms, 48 bonds, 6 residues, 1 model selected
> smiles
> O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
Unknown command: smiles
O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
> open smiles
> O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
'smiles' has no suffix
> open
> smiles:O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
Translated SMILES to 3D structure via NCI web service (SMILES:
O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> select add #2
107 atoms, 110 bonds, 7 residues, 2 models selected
> hide #2 models
> select subtract #2
49 atoms, 48 bonds, 6 residues, 1 model selected
> show #2 models
> show #!1 models
> hide #1.1 models
> hide #!1 models
> show #1.1 models
> select add #2
107 atoms, 110 bonds, 7 residues, 2 models selected
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #!1 models
> select add #1
4308 atoms, 4405 bonds, 2 pseudobonds, 543 residues, 3 models selected
> select subtract #1
58 atoms, 62 bonds, 1 residue, 1 model selected
> hide #1.1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> show #!1 models
> select add #1
4308 atoms, 4405 bonds, 2 pseudobonds, 543 residues, 3 models selected
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #2 target m
> close #2
> open "/Users/lauriewang/Library/CloudStorage/GoogleDrive-
> lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/1. hSec61 Inhibitors
> Project /5. Model Building and Alphafold Structures/Maps/Unsharpened, Local
> Maps/KZR779-Sharpenedmap1(1).mrc"
Opened KZR779-Sharpenedmap1(1).mrc as #2, grid size 600,600,600, pixel 0.83,
shown at level 0.0797, step 4, values float32
> volume #2 level 0.2862
> volume #2 step 1
> volume #2 level -0.06033
> volume #2 level 0.1196
> volume #2 level 0.133
> close #2
> show #1.1 models
> hide #1.1 models
> open /Users/lauriewang/Desktop/cryosparc_P10_J309_007_volume_map.mrc
Opened cryosparc_P10_J309_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.05, shown at level 0.125, step 1, values float32
> volume #2 level 0.3728
> hide #!2 models
> select #1/A$501
Expected an objects specifier or a keyword
> select #1/@$501
Expected an objects specifier or a keyword
> select #1/@501
Expected an objects specifier or a keyword
> select #1/A:501
58 atoms, 62 bonds, 1 residue, 1 model selected
> select /A:501@C18
1 atom, 1 residue, 1 model selected
> select #1/A:501
58 atoms, 62 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> ui tool show "Model Loops"
> select #1/A:501
58 atoms, 62 bonds, 1 residue, 1 model selected
> sequence chain #1/A:501 viewer true
Expected fewer arguments
> sequence chain #1/A:501
Chains must have same sequence
> sequence chain #1/A:501
Chains must have same sequence
>
Unknown command: sequence #1/A:501
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:468
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:468
7 atoms, 6 bonds, 1 residue, 1 model selected
> selection #1/A:501
Unknown command: selection #1/A:501
> select #1/A:501
58 atoms, 62 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> color sel #ff40ff atoms
> color /A:501@C1 blue
> color /A:501@O1 blue
> color /A:501@O01 blue
> color /A:501@O01 red
> structure
> O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
Unknown command: build structure
O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
> start structure
> O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
Unknown command: start structure
O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5
> open "/Users/lauriewang/Library/CloudStorage/GoogleDrive-
> lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/4. Substrate-engaged
> inhibitor bound ChiSec61/3. Structural
> modeling/J327_Sec61-KZR540-coot-3_conf2_real_space_refined_000.pdb"
Chain information for
J327_Sec61-KZR540-coot-3_conf2_real_space_refined_000.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> color #1/A:501@C29
> color #1/A:501@C29 blue
> color #1/A:501@C29@F32 blue
> color #1/A:501@C29@F30@F32 blue
> color #1/A:501@C29@F30@F31@F32 blue
> color #1/A:501@C26@C29@F30@F31@F32 blue
> color #1/A:501@C26@028@C29@F30@F31@F32 blue
> color #1/A:501@C26@O28@C29@F30@F31@F32 blue
> color #1/A:501@C26@C27@O28@C29@F30@F31@F32 blue
> color #1/A:501@C26@C27@O28@C29@F30@F31@F32@C33 blue
> color #1/A:501@C25@C26@C27@O28@C29@F30@F31@F32@C33 blue
> color #1/A:501@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue
> color #1/A:501@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue
> color #1/A:501@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue
> color #1/A:501@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue
> color #1/A:501@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue
> color #1/A:501@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34
> blue
> color
> #1/A:501@C19@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34
> blue
> color
> #1/A:501@C18@C19@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34
> blue
> color
> #1/A:501@N17@C18@C19@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34
> blue
> hide #!1 models
> show #!2 models
> transparency #2 0.5
> show #!1 models
> hide #!2 models
> show #!2 models
> transparency #2 0.1
> transparency #2 0.9
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume zone #2 nearAtoms #1/A:501 range 2 newMap true
Opened cryosparc_P10_J309_007_volume_map.mrc zone as #4, grid size
256,256,256, pixel 1.05, shown at step 1, values float32
> surface dust #3 size 5
No surfaces specified
> surface dust #3 size 5
No surfaces specified
> volume #4 level 0.4534
> color #4 turquoise
> transparency #4 0.9
> transparency #4 0.1
> transparency #4 1
> transparency #4.1 0.9
> select add #4.1
58 atoms, 62 bonds, 1 residue, 2 models selected
> select subtract #4.1
58 atoms, 62 bonds, 1 residue, 1 model selected
> select add #4.1
58 atoms, 62 bonds, 1 residue, 2 models selected
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> dimtransparency #4.1 0.9
Unknown command: dimtransparency #4.1 0.9
> dimtransparency #4 0.9
Unknown command: dimtransparency #4 0.9
> volume #4 style image
> transparency #4 0.9
> transparency #4 0.5
> volume #4 style surface
> volume #4 change image level 3.945e-05,0 level 0.08594,0.8 level 0.8591,1
> volume #4 level 0.3897
> transparency #4 0.9
> surftransparency #4 90%
Unknown command: surftransparency #4 90%
> ~surftransparency #4 90%
Unknown command: ~surftransparency #4 90%
> ~surftransparency #4
Unknown command: ~surftransparency #4
> ~surftransparency
Unknown command: ~surftransparency
> lighting simple
> transparency #4 1
> transparency #4 0.9
> lighting full
> lighting soft
> lighting full
> set bgColor black
> set bgColor white
> lighting simple
> volume #4 level 0.4001
> volume #4 style mesh
> volume #4 style image
> volume #4 style surface
> transparency #4 90
> transparency #4 50
> lighting soft
> hide #4.1 models
> select subtract #4.1
58 atoms, 62 bonds, 1 residue, 1 model selected
> Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green
Unknown command: Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green
> select #1/a:501
58 atoms, 62 bonds, 1 residue, 1 model selected
> Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green
Unknown command: Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green
> color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green
> color #1/A:501@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36 green
> color #1/A:501@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36 green
> color #1/A:501@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 green
> color #1/A:501@C02@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 green
> color #1/A:501@C02@C03@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151
> green
> color #1/A:501@C02@C03@C04@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151
> green
> color
> #1/A:501@C02@C03@C04@C05@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151
> green
> color
> #1/A:501@C02@C03@C04@C05@C06@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151
> green
> color
> #1/A:501@C02@C03@C04@C05@C06@N07@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151
> green
> color
> #1/A:501@C02@C03@C04@C05@C06@N07@C08@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151
> green
> color #1/A:501@C09 blue
> color #1/A:501@C09@C10 blue
> color #1/A:501@C09@C10@C11 blue
> color #1/A:501@C09@C10@C11@N12 blue
> color #1/A:501@C09@C10@C11@N12@C13 blue
> color #1/A:501@C09@C10@C11@N12@C13@C14 blue
> show #4.1 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> color /A:62-71 violet
> color /A:292,183,179,81,85 saddle brown
> lighting soft
> color /A:501@O01 orange
> volume #4 level 0.1819
> volume #4 level 0.2884
> hide #4.1 models
> color /A:501@O01@N17 orange
> select #1/A:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:69-80
86 atoms, 85 bonds, 12 residues, 1 model selected
> select #1/A:64
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:64
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:65-68
34 atoms, 33 bonds, 4 residues, 1 model selected
> select #1/A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:68-69
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:68-69
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:70
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:70-71
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> volume #2 level 0.4989
> volume #2 level 0.3788
> volume #2 level 0.4764
> hide #!4 models
> show #!4 models
> hide #!2 models
> volume #2 level 0.3969
> volume #2 level 0.7676
> volume #2 level 0.4884
> volume #2 level 0.4419
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> hide #!2 models
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/A:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:58-62
37 atoms, 38 bonds, 5 residues, 1 model selected
> select #1/A:70
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:70-73
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #1/A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:66-70
39 atoms, 38 bonds, 5 residues, 1 model selected
> select #1/A:173
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:173-182
71 atoms, 72 bonds, 10 residues, 1 model selected
> select #1/A:173
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:173-174
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:174
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:174
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:170-184
106 atoms, 107 bonds, 15 residues, 1 model selected
> select #1/A:177
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:177-180
24 atoms, 23 bonds, 4 residues, 1 model selected
> select #1/A:178
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:178
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:173
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:173-174
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:183-185
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/A:182
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:182
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:180-181
14 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:178
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:178
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:184
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:184-185
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/A:185
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:185
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:182-183
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/A:182
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:180-184
38 atoms, 38 bonds, 5 residues, 1 model selected
> select #1/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:181-182
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/A:182-183
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/A:182-184
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/A:184
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:184
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:185
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:185-186
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:186-187
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 16 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 27 days 1:21
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in Qt event loop: QPainter::begin: Paint device returned engine == 0, type: 3 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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